Literature DB >> 21460082

Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313.

Lawrence Feinberg1, Justine Foden, Trisha Barrett, Karen Walston Davenport, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Alla Lapidus, Susan Lucas, Jan-Fang Cheng, Samuel Pitluck, Tanja Woyke, Natalia Ivanova, Natalia Mikhailova, Miriam Land, Loren Hauser, D Aaron Argyros, Lynne Goodwin, David Hogsett, Nicky Caiazza.   

Abstract

Clostridium thermocellum DSM1313 is a thermophilic, anaerobic bacterium with some of the highest rates of cellulose hydrolysis reported. The complete genome sequence reveals a suite of carbohydrate-active enzymes and demonstrates a level of diversity at the species level distinguishing it from the type strain ATCC 27405.

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Year:  2011        PMID： 21460082      PMCID： PMC3133140          DOI： 10.1128/JB.00322-11

Source DB:  PubMed          Journal:  J Bacteriol        ISSN： 0021-9193            Impact factor:   3.490


  10 in total

Review 1.  Microbial cellulose utilization: fundamentals and biotechnology.

Authors:  Lee R Lynd; Paul J Weimer; Willem H van Zyl; Isak S Pretorius
Journal:  Microbiol Mol Biol Rev       Date:  2002-09       Impact factor: 11.056

2.  Solexa Ltd.

Authors:  Simon Bennett
Journal:  Pharmacogenomics       Date:  2004-06       Impact factor: 2.533

3.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

4.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

Review 5.  How biotech can transform biofuels.

Authors:  Lee R Lynd; Mark S Laser; David Bransby; Bruce E Dale; Brian Davison; Richard Hamilton; Michael Himmel; Martin Keller; James D McMillan; John Sheehan; Charles E Wyman
Journal:  Nat Biotechnol       Date:  2008-02       Impact factor: 54.908

6.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

Authors:  B Ewing; L Hillier; M C Wendl; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

7.  Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors:  B Ewing; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

8.  Consed: a graphical tool for sequence finishing.

Authors:  D Gordon; C Abajian; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

9.  Deletion of the Cel48S cellulase from Clostridium thermocellum.

Authors:  Daniel G Olson; Shital A Tripathi; Richard J Giannone; Jonathan Lo; Nicky C Caiazza; David A Hogsett; Robert L Hettich; Adam M Guss; Genia Dubrovsky; Lee R Lynd
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-13       Impact factor: 11.205

10.  Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant.

Authors:  Shital A Tripathi; Daniel G Olson; D Aaron Argyros; Bethany B Miller; Trisha F Barrett; Daniel M Murphy; Jesse D McCool; Anne K Warner; Vineet B Rajgarhia; Lee R Lynd; David A Hogsett; Nicky C Caiazza
Journal:  Appl Environ Microbiol       Date:  2010-08-06       Impact factor: 4.792
  10 in total
  26 in total

1.  Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2.

Authors:  Steven D Brown; Raphael Lamed; Ely Morag; Ilya Borovok; Yuval Shoham; Dawn M Klingeman; Courtney M Johnson; Zamin Yang; Miriam L Land; Sagar M Utturkar; Martin Keller; Edward A Bayer
Journal:  J Bacteriol       Date:  2012-06       Impact factor: 3.490

2.  Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase.

Authors:  Yanning Zheng; Jörg Kahnt; In Hyuk Kwon; Roderick I Mackie; Rudolf K Thauer
Journal:  J Bacteriol       Date:  2014-08-25       Impact factor: 3.490

3.  Characterization of all family-9 glycoside hydrolases synthesized by the cellulosome-producing bacterium Clostridium cellulolyticum.

Authors:  Julie Ravachol; Romain Borne; Chantal Tardif; Pascale de Philip; Henri-Pierre Fierobe
Journal:  J Biol Chem       Date:  2014-01-22       Impact factor: 5.157

Review 4.  Cellulolytic thermophilic microorganisms in white biotechnology: a review.

Authors:  Kalpana Sahoo; Rajesh Kumar Sahoo; Mahendra Gaur; Enketeswara Subudhi
Journal:  Folia Microbiol (Praha)       Date:  2019-05-17       Impact factor: 2.099

Review 5.  Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum.

Authors:  Wolfgang H Schwarz; Roman Brunecky; Jannis Broeker; Wolfgang Liebl; Vladimir V Zverlov
Journal:  World J Microbiol Biotechnol       Date:  2018-02-26       Impact factor: 3.312

6.  CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum.

Authors:  Wei Xiong; Paul P Lin; Lauren Magnusson; Lisa Warner; James C Liao; Pin-Ching Maness; Katherine J Chou
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-28       Impact factor: 11.205

7.  Comparative quantitative analysis of gene expression profiles of glycoside hydrolase family 10 xylanases in the sheep rumen during a feeding cycle.

Authors:  Zhongyuan Li; Heng Zhao; Peilong Yang; Junqi Zhao; Huoqing Huang; Xianli Xue; Xinshang Zhang; Qiyu Diao; Bin Yao
Journal:  Appl Environ Microbiol       Date:  2012-12-07       Impact factor: 4.792

8.  Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus.

Authors:  Daehwan Chung; Joel Farkas; Janet Westpheling
Journal:  J Ind Microbiol Biotechnol       Date:  2013-03-10       Impact factor: 3.346

9.  Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways.

Authors:  Douwe van der Veen; Jonathan Lo; Steven D Brown; Courtney M Johnson; Timothy J Tschaplinski; Madhavi Martin; Nancy L Engle; Robert A van den Berg; Aaron D Argyros; Nicky C Caiazza; Adam M Guss; Lee R Lynd
Journal:  J Ind Microbiol Biotechnol       Date:  2013-05-05       Impact factor: 3.346

10.  Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains.

Authors:  Beth Papanek; Kaela B O'Dell; Punita Manga; Richard J Giannone; Dawn M Klingeman; Robert L Hettich; Steven D Brown; Adam M Guss
Journal:  J Ind Microbiol Biotechnol       Date:  2018-09-05       Impact factor: 3.346
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